It does affect clipnodes, but a clip brush isn't a node itself. See a clipnode as a convex 3D passable block, the player can only walk through clipnodes. By covering complex solid brushes with a clip brush, you prevent them from splitting the rooms clipnode up into many small clipnodes, creating only a few instead.
It's like face splitting, but 3D volume splitting instead. A simpler clipping hull means shorter compile time and faster in-game behaviour, theoretically. The in-game gain is usually not really significant, but since we lack specific profiling tools for HL there's no way to tell.
It's one of the reasons I'd recommend to make small detailed brushes func_illusionaries rather than func_walls, or to cover them with clip brushes.